[gmx-users] B-factor calculations

[David van der Spoel]

Jon Ellis wrote:
> Hello users
> 
> I am using B-factors to look at protein flexibility, using g_rmsf. I 
> have a 3-ns simulation of an RNA strand bound to a 30-mer peptide. I did 
> g_rmsf on the complex using the -oq option to obtain the bfac.pdb file, 
> which gives me the B-factors averaged over the entire trajectory (I think).
> 
> Is it reasonable and physically valid to calculate b-factors varying 
> over time, say by computing g_rmsf for smaller segments of my 
> trajectory? If so, what would be a reasonable time interval for the 
> averaging?
> 
In principle yes, but 3 ns is not a lot. You may want to try different 
analyses like essential dynamics, and prolong your trajectory.

> Thanks in advance for your help
> 
> Cheers
> Jon
> 
> 
> 
> ----------------------------------------
> Jon Ellis
> PhD Candidate, Thompson Group
> Institute of Biomaterials and Biomedical Engineering/Dept of Chemistry
> University of Toronto
> Lash Miller 147
> (416) 978-6568
> jon.ellis at utoronto.ca
> ----------------------------------------
> 
> 
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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